#' Add Retention Time to a mona.msp
#' @export addRT.mona
#' @param msp A msp file downloaded from MoNA
#' @param prediction a dataframe from RT.spell function
#' @return  msp file with Predicted Retention time
#' @examples
#' \donttest{
#' addRT.mona(msp="MoNA-export-CASMI_2016.msp",mona_rt)}


addRT.mona <- function (msp="mspfile",prediction) {

# Read the MSP file
mspfile <- msp
specfile <- readLines(mspfile, n=-1L)

# Read the RT information

rtvec <- prediction$RTP
names(rtvec) <- prediction$InChIKey



# Loop through each spectra
startind <- grep("Name:", specfile)
endind <- c(startind[-1]-1, length(specfile))

con1 <- file(msp,"w")
for (i in 1:length(startind)) {
  spect <- specfile[startind[i]:endind[i]]

  ik <- gsub("InChIKey: ","",spect[grep("InChIKey:", spect)])

  vec_print <- paste0("RETENTIONTIME: ",rtvec[ik])

  spect1 <- c(spect[1:5],paste0(vec_print), spect[6:length(spect)])

  writeLines(spect1, con1)

  print(i)
}
close(con1)

}


